Microbiology Class Notes: The Big Picture

By Tramar F. Murdock

Microbiology Class Notes takes a comprehensive look at Microbiology and gives one the big picture.
Time for studying is at a premium, and for that reason, it is important to study effectively. Unless one can remember EVERYTHING in Microbiology for the big exam, you want to use these notes. These notes are intended for the Medical, Graduate, Nursing, or Undergraduate student.

• Language: English
• Publisher: AuthorHouse
• Release date: Aug 11, 2015
• ISBN: 9781504924047

Tramar F. Murdock

Tramar F. Murdock, HTL (ASCP), MD was born and raised in Baltimore, Maryland. She is a Pathologist and serves as Owner and Medical Director of Associates in Tissue Technology Inc., located in Baltimore, MD. She is an Adjunct professor in the Department of Natural Science at Coppin State University, teaching Histology, Microbiology, Biological Science, Genetics, and Comprehensive Preview of Anatomy and Physiology. Dr. Murdock is a visiting Pathologist at the Office of the Chief Medical Examiner’s for the State of Maryland. She is graduate of the Geisel School of Medicine at Dartmouth, and completed her residency in Anatomic and Clinical Pathology at the University of Maryland Medical Systems. Dr. Murdock holds a certification in Histotechnology as an HTL,(ASCP). She has given lectures and speaking engagements concerning Histology and Histotechnology at Geisel School of Medicine at Dartmouth and has appeared on Urban Health Beat Radio, speaking on Pathology and Histotechnology. She is a wife, mother, and grandmother. She is an enthusiastic church member, community, political and social activist, and a wonderful cook. Dr. Murdock has published “Histology Class Notes: The Big Picture” and is currently working on publishing “Class Notes,” outlining Histotechnology, as well as developing a Histotechnology Training Program.

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© 2015 Tramar F. Murdock, MD. All rights reserved.

No part of this book may be reproduced, stored in a retrieval system, or transmitted by any means without the written permission of the author.

Published by AuthorHouse 08/07/2015

ISBN: 978-1-5049-2405-4 (sc)

ISBN: 978-1-5049-2404-7 (e)

Library of Congress Control Number: 2015911947

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Contents

Acknowledgements And Special Thanks To

Bibliography

Introduction/Brief History

Chemical Principles/Elements Of Microbiology

Observing Microorganisms

Anatomy Of Prokaryotic And Eukaryotic Cells

Microbial Metabolism

Microbial Growth

Control Of Microbial Growth

Microbial Genetics

Biotechnology And Dna Technology

Classification Of Microorganisms

The Prokaryotes: Domains Bacteria And Archaea

The Eukaryotes

Viruses, Viroids, Prions

Principles Of Disease And Epidemiology

Microbial Mechanisms Of Pathogenicity

Innate Immunity: Nonspecific Defenses Of The Host

Adaptive Immunity: Specific Defenses Of The Host

Practical Applications Of Immunology

Disorders Associated With The Immune System

Antimicrobial Drugs

Microbial Diseases Of The Skin And Eyes

Microbial Diseases Of The Central Nervous System

Microbial Diseases Of The Respiratory System

Microbial Diseases Of The Urinary And Reproductive System

Microbial Diseases Of The Digestive System

Microbial Diseases Of The Cardiovascular And Lymphatic Systems

Environmental Microbiology

Applied And Industrial Microbiology

ACKNOWLEDGEMENTS AND SPECIAL THANKS TO

Garry S. Jennings, MD

QOL Pain Management, Inc.

Friend, Husband, and Supporter

Dr. Elmer Pfefferkorn

Dartmouth Medical School

Microbiology

Mentor

Vincent Memoli, MD

Dartmouth Medical School

Pathology

Friend and Mentor

BIBLIOGRAPHY

1. Gladwin M, Trattler B. Clinical Microbiology Made Ridiculously Simple; 2nd edition. MediMaster, Inc., Miami, 1997.

2. Tortora j, Funke B, Case C, et al. Microbiology: An Introduction; 11th edition. Pearson Education, Inc., publishing as Benjamin Cummings, San Francisco, CA, 2005.

MICROBIOLOGY

INTRODUCTION/BRIEF HISTORY

A. Microbiology

• The study of minute living things (microorganisms) which live around us and /or inside us

• Usually too small to be seen by the unaided eye

B. What is an Organism

• A living thing (animal, plant, single cell)

• Takes in and breaks down food for energy and nutrients; excretes undigested food as waste

• Reproduce

C. Friendly Microorganisms

• Majority of Microorganisms help maintain balance of living organisms and chemicals in the environment

o Flora organisms in the intestines help digest food; help form Vitamins (B, K)

• Used in producing foods, drugs, chemicals, alcohol, enzymes

D. Unfriendly Microorganisms

• Pathogenic microbes: produce disease

• Cause Infection(s): invasion of disease causing microorganisms

o Entameoba histolytica (causes Traveler’s diarrhea)

o Mycobacterium tuberculosis (causes TB)

E. Major Groups

• Bacteria (singular: bacterium)

o Bacteriology: study of Bacteria

o Prokaryotic organisms (simple single-celled/unicellular organisms)

o Genetic material not enclosed in a nuclear membrane

o Reproduce by binary fissure (divide into 2 equal parts)

o Most use organic chemicals for nutrition

o Some manufacture food by photosynthesis

o Some have flagella (motility)

o Cell wall composed of peptidoglycan

o Several shapes and forms

• Archaea

o  Prokaryotic cells

o Cell wall lacks peptidoglycan

o Found in extreme environments

o Three groups: methanogens (produce methane), halophiles (salt loving), extreme thermophiles (heat)

• Viruses (singular: virus)

o Virology: study of viruses

o Submicroscopic, acellular, parasitic entities made up of a core of DNA or RNA, surrounded by a protein coat

o Reproduce only by using the Host cellular machinery

• Fungi (singular: fungus)

o Mycology: study of Fungi

o Eukaryotic (cells have a distinct nucleus containing DNA surrounded by a nuclear membrane)

o Unicellular or multicellular

o Cell wall composed of substance called chitin

o Do not carry out photosynthesis

o Yeast, molds, mushrooms

• Algae (singular: alga)

o Phycology: study of Algae

o Eukaryotic Photosynthetic organisms

o Cell wall of many composed of cellulose

o Abundant in freshwater, saltwater, soil, and associated with plants

o Do not generally require organic compounds from the environment

o Produce oxygen and carbohydrates used by other organisms

• Protozoa (singular:protozoan)

o Protozoology: study of Protozoa

o Animal-like unicellular eukaryotic organisms

o Found in aquatic and terrestrial places

o Some photosynthetic

o Move by pseudopods, flagella, or cilia

o Ingest or absorb organic compounds

• Parasites

o Parasitology: study of parasites

o Lives at the expense of another organism or host

o Worms (helminths), insects, certain bacteria, viruses

F. Naming and Classification of Microorganisms

• Naming:Carl Linnaeus (1735)

o Used Two Names (Latin)

■ 1st name: Genus (plural genera); always CAPITALIZED

■ 2nd name: Specific epithet (species name); not capitalized

■ Both names underlined or italicized

Staphylococcus aureus

clustered    circular    golden

Escherichia coli

Theodor Escherich    lives in colon

• Classification: Carl Woese (1978)

o Based on molecular and cellular characteristics

o Three Domains

■ Bacteria: peptidoglycan cell walls

■ Archaea: lack peptidoglycan in cell wall (if cell wall present)

■ Eukarya:Organisms from the following kingdoms

✓ Protists: algae, protozoa, slime molds

✓ Fungi: unicellular yeasts, multicellular molds, mushrooms

✓ Plants: moss, conifers, ferns, flowering plants

✓ Animals: insects, sponges, worms, vertebrates

G. First Observations

• Zacharias Janssen (1590)

o Believed to have developed first Compound Microscope (3 tubes)

• Robert Hooke (1665)

o Viewed slices of cork (non living) and saw little boxes which he called cells

o Lead to development of Cell Theory

• Antoni Van Leeuwenhoek (1673)

o Improved Hooke’s microscope

o First person to view a living organism (Animalcules)

H. Spontaneous versus Non-Spontaneous Generation

• Spontaneous Generation

o Originally thought some living organisms arouse from non-living matter

• Non-Spontaneous Generation

o Francesco Redi (1668)

■ Proved organisms did not spontaneously appear

■ Experiment with jars containing decayed meat

o John Needham (1745)

■ Microbes arise from heated nutrient fluids (chicken and corn broth), after covered and cooled

o Lazzaro Spallanzani (1765)

■ Nutrient fluids heated after being covered did not grow microbes; microbes in air entered

I. Theory of Biogenesis

• Rudolf Virchow (1858)

o Living cells come from preexisting living cells

• Louis Pasteur (1861)

o Microorganisms are present in the air, nonliving matter, and contaminate sterile things

■ Aseptic technique

J. Fermentation and Pasteurization

• Methods used to prevent spoilage

o Pasteurization: a technique which kills most bacteria that cause spoilage by heating to a certain temperature

o Fermentation:anaerobic (without oxygen) cellular process in which organic foods are converted into simpler compounds, and chemical energy is produced; occurs in certain bacteria, yeast

■ Converts sugar to acids, gases, and/or alcohol, in the absence of air

K. Germ Theory of Disease

• A Contagion (microorganism) can cause a disease

o Agostino Bassi (1835): identified a fungus causing silkworm disease

o Louis Pasteur (1865): protozoan afflicting silkworm moths causing disease

o Joseph Lister (1867): used carbonic acid (phenol) for surgical wounds

• Robert Koch (1876)

o Koch’s postulates

o Proved specific microorganisms caused specific diseases

■ Bacillus anthracis causes the disease Anthrax

L. Vaccination

• Edward Jenner (1796)

o Inoculated healthy person with tiny amount of disease causing organisms

o Inoculation with cowpox provided humans immunity to smallpox

o Protection from a disease provided by vaccination called immunity

• Vaccines produced from: living avirulent microbes, killed pathogens, parts of virulent microbes, and recombinant DNA techniques

M. Birth of Modern Chemotherapy

• Chemotherapy

o Treatment of infectious (microbes) and noninfectious (cancers) diseases using chemical substances

o Drug that will kill pathogen without harming the infected host

■ Synthetic drugs: prepared from chemicals in the lab

✓ Paul Ehrlich (1890)

✓ Salvarsan (arsenic derivative) effective against syphilis

✓ Quinine-malaria

✓ Sulfonamides (sulfa drug)-bacterial infections

■ Antibiotics-chemicals produced naturally by bacteria or fungi

◊ Alexander Flemming

• Problems with Synthetic Drugs and Antibiotics

o Toxicity

o New Strains emerging

N. Genomics

• The study of an organisms genes to help classify bacteria, fungi, protozoan

• Recombinant DNA Technology

o Technique using fragments of DNA (human/animal) that code for certain proteins (genes) and attach these genes to bacterial DNA

o The recombinant DNA is inserted into bacteria (or other microbes); used to make large quantities of the desired protein

O. Microbes and Human Welfare

• The majority of microbes benefit humans, animals, plants

o Recycling: microbes recycle elements between soil and the atmosphere

■ Microbial Ecology

o Sewage Treatment: recycle water

o Bioremediation: microbes used to clean up pollutants and toxic waste

o Insect Pest Control: important for agricultural

o Biotechnology and Recombinant DNA Technology:commercial use of microbes to produce common foods and chemicals

■ Gene Therapy: inserting a missing gene or replacing defective one

P. Microbes and Human Disease

• Normal Microbiota

o Outside and inside the Body

o Normal microbiota (flora), DO NOT HARM US!

• Biofilms

o Complex aggregrate of microbes

o Beneficial (protective layer, food) or harmful (cause infections, clog pipes)

• Infectious Disease

o Pathogens invade host causing disease

• Emerging Infectious Diseases (EIDs)

o Certain infectious diseases are reemerging and increasing

o Due to evolutionary changes

■ H1N1 influenza (flu)

■ Avian influenza (H5N1)or bird flu

■ Methicillin-resistant Staphylococcus aureus(MRSA)

■ Vancomycin-resistant Staphylococcus aureus(VRSA)

• Emerging Infectious Diseases (EIDs)

o West Nile encephalitis (WNE)

o Bovine spongioform encephalopathy (BSE or mad cow disease)

o Ebola hemorrhagic fever (EHF)

o Human immunodeficiency virus (HIV)

MICROBIOLOGY

CHEMICAL PRINCIPLES/ELEMENTS OF MICROBIOLOGY

A. Microorganisms are made up of Chemicals

• An organism is also known as A Chemical Processing Plant

• Take things, brake them down, rearrange these things into forms which provide nutrients andenergy

• Chemistry is the science of the interactions between atoms and molecules

B. Chemical Elements and the Atom

•  All matter (rock, air, living organisms) is made up of Atoms

ThinkstockPhotos-464049089.jpg

•  Atom is the smallest unit of a chemical element

•  Consist of

o  Nucleus: central, usually stable; consists of proton (+) and neutron (o)

o  Shell: outer, surrounds nucleus; consist of electrons (-) moving around nucleus; region of different energy levels

•  Atoms listed by their atomic number : # protons in nucleus

•  Atomic weight: total # of protons and neutrons

• Chemical Element (s)

o A pure chemical substance consisting of a single atom distinguished by its atomic number

■ Example : Carbon (C)

o Isotopes: atoms with different #’s of neutrons, but same # protons in the nucleus

■ Cause difference in atomic weights

■ Example: Oxygen (O); has three isotopes

• Electronic Configurations

o Consists of electrons arranged around the nucleus in electron shells

o Each shell holds a maximum # of electrons

o Filled shells: Stable, inert

o Outer electron shell partially filled: Unstable, reacts

C. Chemical Reaction (s)

• Process of bonding together atoms and separating atoms already bonded

• Occurs by gaining, losing, or sharing electrons from outer shell

• Rearranging, combining, separating elements

• Requires energy

• Chemical reactions

o Endergonic: absorbs more energy that expels

o Exergonic: expels (releases) more energy than absorbed

• Three (3) Types of Chemical Reactions

o Synthesis: 2 or more atoms, ions, molecules bind together forming a larger molecule

■ Anabolic/Anabolism

A + B 3350.png AB

o Decomposition: breaks down into smaller parts

■ Catabolic/Catabolism

AB 3348.png A + B

o Exchange/Displacement

■ Anabolic and Catabolic

AB + C 3346.png AC + B

AB + CD 3344.png AC +BD

D. Reversibility of Chemical Reactions

• Occur in either direction

o A + B 3342.png AB

■ Due to reactants and products being unstable

■ Special conditions

E. Chemical Bond (s)

• Causes stabilization

o Diatomic: 2 atoms of the same element bond (H-H= H2)

o Compound: 2 atoms of different chemical elements bind (H-O-H=H2O)

• Chemical Bonds can be:

o Ionic: attraction between ions of opposite charge

■ Ex. NaCl

o Covalent: atoms share one or > pairs of electrons; strong bonds

■ Ex. H2

o Hydrogen :weak temporary bond; a hydrogen atom bonded to one oxygen or nitrogen atom is attracted to another oxygen or nitrogen atom; bridge between different molecules

■ Ex. H2O

• Molecular Weight and Moles

o Molecular weight: the sum of the atomic weighs of all its atoms

o Mole: is the molecular weight expressed in grams

F. Chemical Compounds

• Divided into Groups

o Inorganic: lack carbon (C) molecule; ionic bonds significant

o Organic: contains carbon and hydrogen; covalent bonds significant

• Inorganic Compounds

o Water

■ Most important and most abundant

■ Required for life: growth, repair, reproduction

■ A polar molecule

• Inorganic Compounds

o Acids

■ Dissociates into 1 or > Hydrogen ions (H+) and 1 or > negative ions (anions); a proton donor

o Bases

■ Dissociates into 1 or > positive ions (cations) plus 1 or > negative OH- ions: an electron acceptor

o Salts

■ Dissociates into 1 or > cations (+) and anions(-) ions, in H2O

■ The (+) or (-) ions are neither H+ or OH-

o Acid-Base Balance: pH Concept

■ The pH scale: measures acidity or alkalinity of a substance

✓ pH 7: neutral

✓ pH < 7: acid

✓ pH >7: base

■ Buffer: either releases (H+) or binds (H+) to stabilize pH

• Organic Compounds

o Contain carbon and hydrogen elements

o Carbon plays vital role in living things

o Large organic compounds called polymers

o Polymers: made up of small molecules (monomers)

o Large organic compound called a macromolecule (aka polymer)

o Four Groups of Organic Molecules

■ Carbohydrates

✓ Include sugar, starches, cellulose, glycogen

✓ Made up of carbon, hydrogen, oxygen atoms

✓ Monosaccharides

◊ Simple sugars

◊ Glucose, fructose, galactose, D (deoxyribose)NA, R (ribose)NA

✓ Disaccharides

◊ Two monosaccharides bond

◊ Sucrose:

◊ Lactose:

◊ Maltose:

✓ Polysaccharides

◊ Tens or hundreds of monosaccharides bond

◊ Glycogen, starch, cellulose, chitin, dextran

■ Lipids

✓ Fats which provide protection, insulation, energy

✓ Important to cell membranes

✓ Simple Lipids

◊ Triglycerides

-Contain glycerol and fatty acids; mostly insoluble

-Important in plasma membrane

-Protect and insulate body

-Saturated versus Unsaturated

✓ Complex Lipids

◊ Phospholipids

*Contain glycerol, 2 fatty acids, phosphate group

*Build cell membrane

◊ Glycolipids

*Lipid with carbohydrates attached

✓ Steroids

◊ Cholesterol and some hormones

*Structurally different from lipids

*Important component of plasma membrane

■ Proteins

✓ Contain carbon, hydrogen, oxygen, nitrogen (some sulphur)

✓ Hundreds of different proteins found in a cell

✓ Some are antibodies that kill bacteria, transporters, enzymes, toxins

✓ Make up cell structures, cytoplasmic organelles, movement, hormones

✓ Made up of amino acids which are bonded together by peptide bonds

✓ Four Structural Levels

◊ Primary: aa’s linked to form a polypeptide chain

◊ Secondary: localized, repetitious twisting or folding of the polypeptide chain; helix or pleated sheets

◊ Tertiary: three-dimensional folding of the structure

◊ Quaternary: several polypeptide chains that make up a protein

✓ Have many roles in a living organism

✓ Muscle contraction

✓ Hemoglobin

✓ Motility

■ Nucleic acids

✓ First discovered in the nuclei of cells

✓ Made up of nucleotides (consisting of a base, sugar, phosphate group)

✓ 2 Types

◊ DNA

* Deoxyribose

*Double stranded (ds); forms a double helix; organized into segments (gene)

*Bases: A, G, C, T

*Stores genetic information

◊ RNA

*Ribose

*Single stranded (ss)

*Bases: A, G, C, U

*Function in protein synthesis

G. Adenosine Triphosphate (ATP) Molecules

• Principle energy-carrying molecule

• Stores and supplies energy

• High energy molecule

• Supplies energy for:

o Examples

■ Flagella

■ Moving chromosomes

■ Transports substances in and out of the plasma membrane

• Synthesized from ADP and P

• Releases energy in the form of ADP and P

MICROBIOLOGY

OBSERVING MICROORGANISMS

A. Metric System

• Used to measure microorganisms

• Standard unit of length: the meter (m)

B. Microscopy: The Instruments

• Microscopes are devices that enlarge objects using a process called magnification

• Simplest microscope is a magnifying glass

C. Light Microscopy

• Uses visible light to examine specimens

• Simple: consist of a single lens

• Compound: consists of multiple lenses (ocular and objective)

o Parts of a compound light microscope

■ Frame

✓ Arm:

✓ Base:

✓ Body:

■ Stage

✓ Supports the microscopic slide; may have a clamping device

■ Illuminator

✓ Light source

■ Condenser

✓ Condenses, collects, and directs light from light source to slide

■ Diaphragm

✓ Adjust amount of light that reaches the specimen

■ Objectives

✓ Two or more lenses

✓ Closest to specimen; attached to nose piece (10X, 45X, 100X-oil)

■ Ocular

✓ Eye piece; specimen magnified again

■ Focusing knobs

✓ Brings objects into focus

◊ Coarse adjustment

◊ Fine adjustment

• Total Magnification

o Used to calculate the total magnification of a specimen

o Multiply the objective lens power (Example: 10X, 45X, 100X) by the ocular lens power (factor of 10)

• Resolution

o Also called resolving power

o The ability of the lenses to distinguish fine detail and structure

o The ability of the lenses to distinguish between two points at specified distance apart

o Minimum distance one can see two adjacent objects

• Refractive Index

o A measure of the light-bending ability of the medium

o Changed by staining

o Refracted

o Oil immersion

D. Microscopy

• Bright field

o Stained specimens; brightly illuminated

• Darkfield

o Examines live organisms that are invisible in ordinary light, cannot be stained, or distorted by staining

o Uses a condenser containing an opaque disc which blocks light (light reflected away)

o Specimen is light against a dark background

o Treponema palladium (syphilis)

• Phase-Contrast Microscopy

o Examine detailed internal structures in unstained living microorganisms

o Special diaphragm

• Differential Interference Contrast (DIC)

o Uses two beams of light separated by prisms

o Specimen appears colored due to prism effect (3D images)

• Fluorescence Microscopy

o Uses UV light to illuminate specimens

o Fluorescent dyes called fluorchromes used

o Stains microbes bright apple green, or bright yellow

o Mycobacterium tuberculosis (tuberculosis)

o For immunofluorescence techniques

• Confocal Microscopy

o Uses fluorochromes; uses a pinhole aperature

o Illuminated with short wavelength light

o Used with computers to produces two and three-dimensional images; see inside cell

o Uses lasers

• Two-Photon Microscopy (TPM)

o Living specimen dyed with fluorescent dye

o Uses long-wave (red) light therefore two photons needed

o Can track cell activity in real time

• Scanning Acoustic Microscopy (SAM)

o Uses a sound wave that travels through the specimen to examine living cells

o Study living cells attached to another surface (biofilms)

• Electron Microscopy

o Examines viruses and internal structures of microorganisms (<0.2 μm)

o Uses beams of electrons on the specimen (in a vacuum)

o Instead of glass lens, uses electromagnetic lenses

o Microscopic photographs called micrographs

o Two Types

■ Transmission Electron Microscope (TEM)

✓ Structures smaller than 0.2 μm can be examined

✓ Examine ultra thin section of specimen

✓ Image produced is two-dimensional

✓ Examine viruses or internal structures

■ Scanning Electron Microscope (SEM)

✓ Image produced is three-dimensional

✓ Studies surface features of cells and viruses

• Scanned-Probe Microscopy

o Uses thin metal probe which scans a specimen

o Produces bumps and depressions of the atoms on the surface of the specimen

o Provides detailed views of molecules inside cells

o Two Types

■ Scanning Tunneling Microscopy (STM)

✓ Provide detailed views of molecules such as DNA

■ Atomic Force Microscopy (AFM)

✓ Uses metal-and-diamond probe on specimen

✓ Provides images of molecular processes and biological molecules

E. Preparing Specimens for Light Microscopy